added getStudies and tests

jjjermiah · Feb 3, 2024 · 6e9138a · 6e9138a
1 parent e4df33e
commit 6e9138a
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Showing 3 changed files with 26 additions and 4 deletions.
diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py
@@ -216,6 +216,18 @@ def getBodyPartCounts(
             )
         return bodyparts
 
+    def getStudies(self, Collection : str, PatientID : str = "", StudyInstanceUID : str = ""
+) -> Union[list[dict[str, str]], None]:
+        PARAMS = self.parsePARAMS(locals())
+
+        response = self.query_api(endpoint=NBIA_ENDPOINTS.GET_STUDIES, params=PARAMS)
+
+        if not isinstance(response, list):
+            self.log.error("Expected list, but received: %s", type(response))
+            return None
+
+        return response
+
     def getSeries(
         self,
         Collection: str = "",
@@ -359,8 +371,9 @@ def parsePARAMS(self, params: dict) -> dict:
 
     client = NBIAClient(log_level="info")
 
-    all = client.getCollections()
-    pprint(all)
+    print(client.getStudies(Collection="TCGA-GBM"))
+    # all = client.getCollections()
+    # pprint(all)
 
-    sub = client.getCollections(prefix="aCrin")
-    pprint(sub)
+    # sub = client.getCollections(prefix="aCrin")
+    # pprint(sub)
diff --git a/src/nbiatoolkit/utils/nbia_endpoints.py b/src/nbiatoolkit/utils/nbia_endpoints.py
@@ -19,6 +19,8 @@ class NBIA_ENDPOINTS(Enum):
     GET_BODY_PART_PATIENT_COUNT = "getBodyPartValuesAndCounts"
     GET_NEW_PATIENTS_IN_COLLECTION = "NewPatientsInCollection"
 
+    GET_STUDIES = "v2/getPatientStudy"
+
     GET_SERIES = "v2/getSeries"
     DOWNLOAD_SERIES = "v2/getImageWithMD5Hash"
 

diff --git a/tests/test_nbia.py b/tests/test_nbia.py
@@ -98,6 +98,13 @@ def test_getPatientsByCollectionAndModality(nbia_patientsByCollectionAndModality
     assert isinstance(nbia_patientsByCollectionAndModality[0], str)
     assert len(nbia_patientsByCollectionAndModality[0]) > 0
 
+def test_getStudies(nbia_client, nbia_collections):
+    studies = nbia_client.getStudies(Collection=nbia_collections[0])
+    assert studies is not None
+    assert isinstance(studies, list)
+    assert len(studies) > 0
+    assert isinstance(studies[0], dict)
+
 def test_getSeries(nbia_client, nbia_collections, nbia_patients):
     seriesList = nbia_client.getSeries(
         Collection=nbia_collections[0],